Two regeneration systems were established by using sterile leaves of wild Lycium ruthenicum. The direct organogenesis is differentiated by leaves, and the indirect organogenesis is differentiated by calli. The genetic stability of the regenerated plantlets was assessed by the ISSR markers and flow cytometry(FCM). The results showed that: (1) the best medium for callus induction was MS+1.5 mg·L^-1 2,4D, with induction rate of 100%; the optimum medium for callus differentiation was MS+1.5 mg·L^-1 6BA+0.1 mg·L^-1 IBA, with 39.4 shoots per gram of calli. (2) The suitable medium for direct shoot induction was MS+0.5 mg·L^-1 6BA+0.3 mg·L^-1 NAA, with induction rate of 92.9%, and 18.1 shoots per explant. (3) After adventitious buds were transferred to the MS medium without hormones, the roots could form within two weeks. (4) FCM results showed that parental plantlets and regenerated plantlets were diploid. (5)ISSR analysis showed that the average genetic similarity coefficients of indirect and direct regenerated plantlets were 0.84 and 0.91. The direct organogenesis was a more effective method for plant regeneration of L. ruthenicum.